CRISPR Guide Finder
How to find CRISPR guides
- Paste the DNA you want to cut, as plain text or FASTA.
- Choose the nuclease and its PAM, or type your own, and set the guide length.
- Set the GC range and whether to drop guides with a TTTT run.
- Every guide is listed with its position, strand, sequence, PAM and GC content. Copy output or Download saves the result.
Frequently asked questions
What is a PAM?
A short motif the nuclease has to sit on next to its target. SpCas9 needs NGG right after the 20 nt guide; Cas12a needs TTTV right before a longer one. No PAM, no cut.
Which GC content should I aim for?
Between 35% and 75% works for most guides, with 40% to 60% the usual sweet spot. Very low GC binds weakly and very high GC raises off-target cutting.
Why drop guides with TTTT?
A run of four or more T bases can act as a termination signal for the U6 promoter used to express the guide, so the sgRNA comes out truncated.
What does the seed column mean?
How many other places in the sequence you pasted carry the same 12 bases next to the PAM. Anything above zero means the guide is not unique even in this sequence, so check it against the whole genome before ordering.
Does this check the genome for off-targets?
No. It only searches the sequence you paste, because a genome-wide search needs the genome. Use it to shortlist guides, then score the shortlist against your organism.
Is my sequence uploaded?
No. Everything runs in your browser, so your sequences never leave your device.